Abstract: Bioinformatics methods were used to analyze the onion（Allium cepa L.）transcriptome SSR loci information and designed simple sequence repeat（SSR）primers，so as to provide a powerful tool for screening onion molecular marker assisted breeding. Five thousand nine hundred and fifty-nine SSR loci（5.10%）were obtained from 106 932 unigenes（84.04 Mb）by using MISA software to screen the onion transcriptome sequencing，and its frequency was 1/14.1 kb. Trinucleotide repeat was the main type，accounted for as much as 37.27% of all SSRs. The AAG/CTT were the predominant repeat types（10.20%），followed by mononucleotide repeat motif（30.91%）and dinucleotide repeat motif（24.75%）. Five thousand two hundred and fifty-eight pairs of SSR primers were designed using Primer 5. Randomly 20 pairs of primers were selected for PCR amplification，12 amplified on clear and reproducible bands，9 in 24 different types showed polymorphism in onion material. Twenty-four onions plants were divided into 4 groups by UPGMA.

Key words: onion, transcriptome, SSR, primer, polymorphism